Bottom Line:
It is known that miRNA target sites are very short and the effect of miRNA-target site interaction alone appears as being unspecific.We demonstrate that the novel motif can be found in at least one third of all transcripts regulated by miRNAs.Beyond, the novel motif has the impact to improve prediction of miRNA target sites significantly.

ABSTRACTIt is known that miRNA target sites are very short and the effect of miRNA-target site interaction alone appears as being unspecific. Recent experiments suggest further context signals involved in miRNA target site recognition and regulation. Here, we present a novel GC-rich RNA motif downstream of experimentally supported miRNA target sites in human mRNAs with no similarity to previously reported functional motifs. We demonstrate that the novel motif can be found in at least one third of all transcripts regulated by miRNAs. Furthermore, we show that motif occurrence and the frequency of miRNA target sites as well as the stability of their duplex structures correlate. The finding, that the novel motif is significantly associated with miRNA target sites, suggests a functional role of the motif in miRNA target site biology. Beyond, the novel motif has the impact to improve prediction of miRNA target sites significantly.

pone-0006473-g001: RNA motif.Detected novel miRNA target context sequence motif downstream of experimentally supported human miRNA target sites motif as sequence logo plot. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each nucleic acid at that position. Here the motif calculated from the non-redundant sequence set with maximum 65% allowed homology is shown. Noteworthy are the overall high GC content, the strong increase of cytosine nucleotides around the motif position 22 and a peak of guanine residues around motif positions 39.

Mentions:
In a first step, we analyzed the complete 3′-UTR sequence downstream of experimentally supported miRNA target sites with a spacer of 100 nucleotides to the target site as described in Material and Methods and shown in Figure S2. In the resulting non-redundant sequence set of human 3′-UTR sequences, we detected a novel sequence motif shown in Figure 1. This motif could be observed in 21% (12 of 57) of the sequences of the non-redundant sequence set. All hits are statistically significant with probabilities less than 10-5 to occur by chance. The probability of finding an equally well-conserved pattern in random sequences with the same nucleotide- and length distribution was estimated as less than 1.0−46 by the MEME algorithm [22], [23]. Furthermore, the motif is found identically no matter of the applied sequence homology filtering level. A detailed description of the motif along with a position weight matrix is given in File S1.

pone-0006473-g001: RNA motif.Detected novel miRNA target context sequence motif downstream of experimentally supported human miRNA target sites motif as sequence logo plot. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each nucleic acid at that position. Here the motif calculated from the non-redundant sequence set with maximum 65% allowed homology is shown. Noteworthy are the overall high GC content, the strong increase of cytosine nucleotides around the motif position 22 and a peak of guanine residues around motif positions 39.

Mentions:
In a first step, we analyzed the complete 3′-UTR sequence downstream of experimentally supported miRNA target sites with a spacer of 100 nucleotides to the target site as described in Material and Methods and shown in Figure S2. In the resulting non-redundant sequence set of human 3′-UTR sequences, we detected a novel sequence motif shown in Figure 1. This motif could be observed in 21% (12 of 57) of the sequences of the non-redundant sequence set. All hits are statistically significant with probabilities less than 10-5 to occur by chance. The probability of finding an equally well-conserved pattern in random sequences with the same nucleotide- and length distribution was estimated as less than 1.0−46 by the MEME algorithm [22], [23]. Furthermore, the motif is found identically no matter of the applied sequence homology filtering level. A detailed description of the motif along with a position weight matrix is given in File S1.

Bottom Line:
It is known that miRNA target sites are very short and the effect of miRNA-target site interaction alone appears as being unspecific.We demonstrate that the novel motif can be found in at least one third of all transcripts regulated by miRNAs.Beyond, the novel motif has the impact to improve prediction of miRNA target sites significantly.

ABSTRACTIt is known that miRNA target sites are very short and the effect of miRNA-target site interaction alone appears as being unspecific. Recent experiments suggest further context signals involved in miRNA target site recognition and regulation. Here, we present a novel GC-rich RNA motif downstream of experimentally supported miRNA target sites in human mRNAs with no similarity to previously reported functional motifs. We demonstrate that the novel motif can be found in at least one third of all transcripts regulated by miRNAs. Furthermore, we show that motif occurrence and the frequency of miRNA target sites as well as the stability of their duplex structures correlate. The finding, that the novel motif is significantly associated with miRNA target sites, suggests a functional role of the motif in miRNA target site biology. Beyond, the novel motif has the impact to improve prediction of miRNA target sites significantly.